[Neuroimaging] Convert Atlas from 1mm to 2mm
Matthew Brett
matthew.brett at gmail.com
Mon Mar 14 18:41:05 EDT 2016
On Mon, Mar 14, 2016 at 1:35 PM, Ariel Rokem <arokem at gmail.com> wrote:
> A few more ways to do this are tallied in this previous thread:
> https://mail.python.org/pipermail/neuroimaging/2015-December/000656.html
The way I would myself do this (because I usually have nipy installed)
is to use nipy image slicing:
In [1]: import nipy
In [2]: img = nipy.load_image('/Users/mb312/data/mni_icbm152_nlin_asym_09a/mni_icbm152_t1_tal_nlin_asym_09a.nii')
In [3]: img.shape
Out[3]: (197, 233, 189)
In [4]: img.affine
Out[4]:
array([[ 1., 0., 0., -98.],
[ 0., 1., 0., -134.],
[ 0., 0., 1., -72.],
[ 0., 0., 0., 1.]])
In [5]: subsampled = img[::2, ::2, ::2]
In [6]: subsampled.shape
Out[6]: (99, 117, 95)
In [7]: subsampled.affine
Out[7]:
array([[ 2., 0., 0., -98.],
[ 0., 2., 0., -134.],
[ 0., 0., 2., -72.],
[ 0., 0., 0., 1.]])
In [8]: nipy.save_image(subsampled, 'smaller.nii')
Cheers,
Matthew
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